NEW YORK – Several companies with a focus on single-cell analysis are launching new products pairing DNA sequencing with other assay modalities.
Earlier this month, Factorial Biotechnologies, a Bay Area startup, launched Mosaic, a cell partitioning instrument that will first enable single-cell whole-genome DNA sequencing, to be followed by RNA sequencing and multiomic analyses such as proteins and DNA methylation. Initially, the products will be independent assays, said CEO John Wells, but the firm plans to combine them to offer, say, DNA and RNA sequencing simultaneously.
BioSkryb already offers the ResolveOme assay for combined whole-genome and full-length transcriptome sample prep for single-cell sequencing and is launching a more streamlined workflow, as well as targeted single-cell DNA sequencing assays including exome and gene panels. It is planning to offer cell surface protein and DNA methylation assays in the future, CEO Suresh Pisharody said, noting that the firm's services business offers cell surface protein analysis.
Finally, Takara Bio, which has been providing single-cell transcriptome sequencing on its ICell8 platform, has begun an early access program for assays for whole-genome amplification as well as full-length RNA isoform analysis, with commercial launch planned for late in the second quarter.
The product launches suggest that the single-cell DNA sequencing market — currently dwarfed by the single-cell transcriptomics market — is poised for growth. "Customers have been clamoring for the ability to integrate DNA and RNA [data]," said Aaron Llanso, VP of product marketing and strategy at BioSkryb. "It's across the board and for different reasons in different applications," especially oncology, cell and gene therapy, and neuroscience.
The single-cell DNA sequencing market has been around for over a decade now, though uptake has been slow, Llanso said. Some of that is due to the cost of sequencing, which had hovered around $10 per Gb for most of that period.
The explosion of single-cell transcriptomics and cell atlas projects in the last 10 years may have also been a necessary precursor to growth. "Now we're starting to see people want to see transcriptional states in the context of the same cell's genome," Llanso said. "Each cell has its own genome, and tissues acquire mutations at different rates," he explained. Researchers are now asking questions about the impact of a particular mutation or combination of mutations and how they could affect gene expression. "They're clamoring for the ability to integrate DNA and RNA from each cell," he said.
Limits on throughput have likely hampered interest in DNA-focused single-cell research. Until now, single-cell whole-genome DNA sequencing has been restricted to plate-based methods. Mission Bio launched its Tapestri instrument in 2017, which has the ability to isolate 10,000 cells per sample and add protein detection, but offers panels, rather than whole-genome assays. 10x Genomics discontinued its single-cell CNV product in 2020.
Factorial's Wells said his firm's instrument will change that. Mosaic's initial microfluidic chips will be able to prepare about 10,000 cells at a time. "We've gone as low as 1,000 and as high as 100,000" cells, he noted.
"It's very similar to a digital PCR partitioner," he said, adding that it works with the firm's intracellular library prep chemistry to enable single-cell resolution of "any type of NGS experiment you'd want to run."
The library prep is done inside cells to form what Factorial calls a "precursor library" of molecules ready for amplification and barcoding, which happens in the Mosaic partitioner. The workflow does not require beads, Wells noted, and takes about six or seven hours, going from a suspension to single-cell sequencing. The instrument can run three chips at once, and each chip can process four samples with up to 10,000 cells per sample.
Wells declined to disclose pricing, including how much the instrument will cost.
He said the firm is working with two single-cell labs and one pharma company as part of an early-access program, though he declined to disclose them. "We are also interested in additional collaborations where we process samples internally for labs interested in our platform," he added.
He touted the instrument's cell yield as being "way higher than the competition," but declined to provide any metrics. Plate-based methods have high yield, but higher throughput methods have approximately an 80 percent loss, he said. For labs running precious samples, such as solid tumor samples, that loss is unacceptable, he added.
Takara's single-cell DNA sequencing assay will be able to process up to eight samples and recover a total of about 1,500 cells. That's less than what its full-length RNA assay can run: up to 96 samples and up to 100,000 cells per run. "We felt 1,500 cells is what people are looking for," said Bryan Bell, Takara's associate director of market strategy.
The DNA assay is based on Takara's PicoPlex whole-genome amplification method, which uses quasi-random priming and linear amplification. This sets up researchers to do copy number variation analysis, which has historically been the primary use of single-cell DNA sequencing.
Takara is also offering the ability to do "in silico" SNV analysis. Because single cells may not have a sufficient number of reads to call SNVs, Takara's software can cluster similar cells and then pool those reads to make SNV calls.
BioSkryb officials said its streamlined workflow, down to eight hours from three days, should help with throughput, noting that the assay is automatable. Dan Landau, a researcher and oncologist at Weill Cornell Medicine, said his lab has scaled prep for the BioSkryb ResolveOme assay by using robotic dispensing and automated cleanup. For a recent experiment that generated 1,000 single-cell genomes, this took production time down to two weeks from 12 weeks and used fewer reagents and consumables.
All three companies are targeting a similar cluster of application areas. Oncology is the big one, followed by cell and gene therapy and neuroscience. General biomarker discovery in both academia and pharma are important markets for Takara, Bell said, while BioSkryb's Pisharody noted that microbiome research and forensics are other markets his firm has customers in.
"People really like that unbiased discovery," Bell said. "The market is looking for ways to go into experiments with a model system without having predisposed targets or notions."
"The appetite is there," Factorial's Wells said. "In [the discovery research market], whole-genome sequencing is what we had to get working."
"The amount of DNA sequencing done on the clinical front is significant," he added. "It's a very valuable and interesting modality." He noted that Factorial is interested in developing hybrid capture-based panels off its whole-genome amplification, such as 500-gene comprehensive genomic profiling panels in oncology.
While DNA plus RNA combo assays are the short-term focus, the drive toward single-cell multiomics is already there. Protein, methylation, and even metabolomics are of interest to researchers, Bell said. "They really want that, but it has to be at the right scale."